Etiologic Risk Group (see link below): Risk Group 2 (WHO classification)
*Background/Disease Information (sort of like the Intro to your Mini Research Write up): Mycobacterium abscessus is related to the bacterium that cause tuberculosis. Commonly found in the environment like water and soil, it can easily contaminate objects such as medical equipment. Transmission usually occurs due to injections of contaminated substances or contact with contaminated equipment. The bacterium can then enter the human body, causing an infection. The symptoms that manifest once Mycobacterium abscessus infection takes place includes red, swollen skin. Fevers, chills, and general malaise are all signs of possible infection. Chronic lung disease can also originate from this bacterium infection, especially if the victim has a weak immune system. To treat the infection, the pus or infected tissue is first removed, then various antibiotics can be taken for a period of time.
Essentiality of this protein:
Peptidyl-tRNA hydrolase (PTH) is a protein that cleaves the bond between the peptide and tRNA during premature release of tRNA from the ribosome. This is significant in that the bacterium will have a supply of tRNA to use for the next translation. No tRNA will be wasted if a translation process is aborted halfway through. Overall, this enzyme is vital to cell viability. Inhibition of this enzyme will cripple the supply of tRNA Mycobacterium abscessus has for synthesizing more proteins, thus effectively reducing viability.
Essentiality data for probable peptidyl-tRNA hydrolase Pth [Mycobacterium tuberculosis H37Rv] BlastP Identity/Positive: 70%/83%
Rv1014c has essentiality data
Gene/Ortholog: mtu1030 (OG4_12216); Phenotype: essential; Source study: nmpdr
Complex of proteins?: No
Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism)
N/A (There were no orthologous druggable targets)
--Show screenshot of BRENDA enzyme mechanism schematic
Figure 1- Brenda reaction mechanism of peptidyl-tRNA hydrolase
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents): -- link to Sigma (or other company) page for assay (see Sigma links below) -- -or link (or citation) to paper that contains assay information -- links to assay reagents (substrates) pages. --- List cost and quantity of substrate reagents, supplier, and catalog #
Structure Available (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model:
-- For Homology Model option:
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB
---- Query Coverage:
---- Max % Identities:
---- % Positives
---- Chain used for homology:
Current Inhibitors: Expression Information (has it been expressed in bacterial cells): Purification Method: Image of protein (PyMol with features delineated and shown separately): *Amino Acid Sequence (paste as text only - not as screenshot or as 'code'): *length of your protein in Amino Acids Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website Molar Extinction coefficient of your protein at 280 nm wavelength: TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it. *CDS Gene Sequence (paste as text only): *GC% Content for gene: *CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): *GC% Content for gene (codon optimized):
Do Not Need this info for Spring (but still copy these lines to your Target page for now) Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers): (link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):
Target (protein/gene name): Peptidyl-tRNA hydrolase
*NCBI Gene # : 16202917
*Protein ID (NP or XP #): MASS_1138
*Organism (including strain): Mycobacterium abscessus (strain: 50594)
Etiologic Risk Group (see link below): Risk Group 2 (WHO classification)
*Background/Disease Information (sort of like the Intro to your Mini Research Write up):
Mycobacterium abscessus is related to the bacterium that cause tuberculosis. Commonly found in the environment like water and soil, it can easily contaminate objects such as medical equipment. Transmission usually occurs due to injections of contaminated substances or contact with contaminated equipment. The bacterium can then enter the human body, causing an infection. The symptoms that manifest once Mycobacterium abscessus infection takes place includes red, swollen skin. Fevers, chills, and general malaise are all signs of possible infection. Chronic lung disease can also originate from this bacterium infection, especially if the victim has a weak immune system. To treat the infection, the pus or infected tissue is first removed, then various antibiotics can be taken for a period of time.
Link to TDR Targets page (if present): N/A
Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.):
http://www.ncbi.nlm.nih.gov/gene/16202917
Essentiality of this protein:
Peptidyl-tRNA hydrolase (PTH) is a protein that cleaves the bond between the peptide and tRNA during premature release of tRNA from the ribosome. This is significant in that the bacterium will have a supply of tRNA to use for the next translation. No tRNA will be wasted if a translation process is aborted halfway through. Overall, this enzyme is vital to cell viability. Inhibition of this enzyme will cripple the supply of tRNA Mycobacterium abscessus has for synthesizing more proteins, thus effectively reducing viability.
Essentiality data for probable peptidyl-tRNA hydrolase Pth [Mycobacterium tuberculosis H37Rv] BlastP Identity/Positive: 70%/83%
Rv1014c has essentiality data
Gene/Ortholog: mtu1030 (OG4_12216); Phenotype: essential; Source study: nmpdr
Complex of proteins?: No
Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism)
N/A (There were no orthologous druggable targets)
*EC#: 3.1.1.29
Link to BRENDA EC# page:
http://www.brenda-enzymes.org/php/result_flat.php4?ecno=3.1.1.29&Suchword=&organism[]=Mycobacterium+tuberculosis&show_tm=0
-- Show screenshot of BRENDA enzyme mechanism schematic
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):
-- link to Sigma (or other company) page for assay (see Sigma links below)
-- -or link (or citation) to paper that contains assay information
-- links to assay reagents (substrates) pages.
--- List cost and quantity of substrate reagents, supplier, and catalog #
Structure Available (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model:
-- For Homology Model option:
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB
---- Query Coverage:
---- Max % Identities:
---- % Positives
---- Chain used for homology:
Current Inhibitors:
Expression Information (has it been expressed in bacterial cells):
Purification Method:
Image of protein (PyMol with features delineated and shown separately):
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
*length of your protein in Amino Acids
Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website
Molar Extinction coefficient of your protein at 280 nm wavelength:
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
*CDS Gene Sequence (paste as text only):
*GC% Content for gene:
*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):
*GC% Content for gene (codon optimized):
Do Not Need this info for Spring (but still copy these lines to your Target page for now)
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
(link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):